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<h1>Source code for MMTK.MoleculeFactory</h1><div class="highlight"><pre>
<span class="c"># A molecule factory is used to create chemical objects</span>
<span class="c"># in code, without a database definition.</span>
<span class="c">#</span>
<span class="c"># Written by Konrad Hinsen</span>
<span class="c">#</span>
<span class="sd">"""</span>
<span class="sd">Molecule factory for creating chemical objects</span>
<span class="sd">"""</span>
<span class="n">__docformat__</span> <span class="o">=</span> <span class="s">'restructuredtext'</span>
<span class="kn">from</span> <span class="nn">MMTK</span> <span class="kn">import</span> <span class="n">Bonds</span><span class="p">,</span> <span class="n">ChemicalObjects</span>
<span class="c">#</span>
<span class="c"># Molecule factories store AtomTemplate and GroupTemplate objects.</span>
<span class="c">#</span>
<span class="k">class</span> <span class="nc">AtomTemplate</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">element</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">element</span> <span class="o">=</span> <span class="n">element</span>
<span class="k">class</span> <span class="nc">GroupTemplate</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">name</span>
<span class="bp">self</span><span class="o">.</span><span class="n">children</span> <span class="o">=</span> <span class="p">[]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">names</span> <span class="o">=</span> <span class="p">{}</span>
<span class="bp">self</span><span class="o">.</span><span class="n">attributes</span> <span class="o">=</span> <span class="p">{}</span>
<span class="bp">self</span><span class="o">.</span><span class="n">positions</span> <span class="o">=</span> <span class="p">{}</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bonds</span> <span class="o">=</span> <span class="p">[]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">locked</span> <span class="o">=</span> <span class="bp">False</span>
<span class="k">def</span> <span class="nf">addAtom</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom_name</span><span class="p">,</span> <span class="n">element</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Add an atom.</span>
<span class="sd"> :param atom_name: the name of the atom</span>
<span class="sd"> :type atom_name: str</span>
<span class="sd"> :param element: the chemical element symbol</span>
<span class="sd"> :type element: str</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">locked</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"group is locked"</span><span class="p">)</span>
<span class="n">atom</span> <span class="o">=</span> <span class="n">AtomTemplate</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">names</span><span class="p">[</span><span class="n">atom_name</span><span class="p">]</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">atom</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">addSubgroup</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">subgroup_name</span><span class="p">,</span> <span class="n">subgroup</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Add a subgroup.</span>
<span class="sd"> :param subgroup_name: the name of the subgroup within this group</span>
<span class="sd"> :type subgroup_name: str</span>
<span class="sd"> :param subgroup: the subgroup type</span>
<span class="sd"> :type subgroup: str</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">locked</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"group is locked"</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">names</span><span class="p">[</span><span class="n">subgroup_name</span><span class="p">]</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">subgroup</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">addBond</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom1</span><span class="p">,</span> <span class="n">atom2</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Add a bond.</span>
<span class="sd"> :param atom1: the name of the first atom</span>
<span class="sd"> :type atom1: str</span>
<span class="sd"> :param atom2: the name of the second atom</span>
<span class="sd"> :type atom2: str</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">locked</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"group is locked"</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bonds</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">atomNameToPath</span><span class="p">(</span><span class="n">atom1</span><span class="p">),</span>
<span class="bp">self</span><span class="o">.</span><span class="n">atomNameToPath</span><span class="p">(</span><span class="n">atom2</span><span class="p">)))</span>
<span class="k">def</span> <span class="nf">setAttribute</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">value</span><span class="p">):</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">locked</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"group is locked"</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">attributes</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="n">value</span>
<span class="k">def</span> <span class="nf">setPosition</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">vector</span><span class="p">):</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">locked</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"group is locked"</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">positions</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="n">vector</span>
<span class="k">def</span> <span class="nf">getAtomReference</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom_name</span><span class="p">):</span>
<span class="n">path</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">atomNameToPath</span><span class="p">(</span><span class="n">atom_name</span><span class="p">)</span>
<span class="nb">object</span> <span class="o">=</span> <span class="bp">self</span>
<span class="k">for</span> <span class="n">path_element</span> <span class="ow">in</span> <span class="n">path</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">]:</span>
<span class="nb">object</span> <span class="o">=</span> <span class="nb">object</span><span class="o">.</span><span class="n">children</span><span class="p">[</span><span class="nb">object</span><span class="o">.</span><span class="n">names</span><span class="p">[</span><span class="n">path_element</span><span class="p">]]</span>
<span class="n">atom_index</span> <span class="o">=</span> <span class="nb">object</span><span class="o">.</span><span class="n">names</span><span class="p">[</span><span class="n">path</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]]</span>
<span class="n">reference</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">atom_index</span><span class="p">):</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="nb">object</span><span class="o">.</span><span class="n">children</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">AtomTemplate</span><span class="p">):</span>
<span class="n">reference</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="kn">from</span> <span class="nn">MMTK.Database</span> <span class="kn">import</span> <span class="n">AtomReference</span>
<span class="k">return</span> <span class="n">AtomReference</span><span class="p">(</span><span class="n">reference</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">atomNameToPath</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom_name</span><span class="p">):</span>
<span class="n">atom_name</span> <span class="o">=</span> <span class="n">atom_name</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">'.'</span><span class="p">)</span>
<span class="nb">object</span> <span class="o">=</span> <span class="bp">self</span>
<span class="k">try</span><span class="p">:</span>
<span class="k">for</span> <span class="n">path_element</span> <span class="ow">in</span> <span class="n">atom_name</span><span class="p">:</span>
<span class="nb">object</span> <span class="o">=</span> <span class="nb">object</span><span class="o">.</span><span class="n">children</span><span class="p">[</span><span class="nb">object</span><span class="o">.</span><span class="n">names</span><span class="p">[</span><span class="n">path_element</span><span class="p">]]</span>
<span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="n">AtomTemplate</span><span class="p">):</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"no atom "</span> <span class="o">+</span> <span class="n">atom</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"no atom "</span> <span class="o">+</span> <span class="s">'.'</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">atom_name</span><span class="p">))</span>
<span class="k">return</span> <span class="n">atom_name</span>
<span class="k">def</span> <span class="nf">writeXML</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">file</span><span class="p">,</span> <span class="n">memo</span><span class="p">):</span>
<span class="k">if</span> <span class="n">memo</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="bp">False</span><span class="p">):</span>
<span class="k">return</span>
<span class="n">names</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="p">)</span><span class="o">*</span><span class="p">[</span><span class="bp">None</span><span class="p">]</span>
<span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">names</span><span class="p">:</span>
<span class="n">names</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">names</span><span class="p">[</span><span class="n">name</span><span class="p">]]</span> <span class="o">=</span> <span class="n">name</span>
<span class="n">atoms</span> <span class="o">=</span> <span class="p">[]</span>
<span class="n">subgroups</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="p">)):</span>
<span class="nb">object</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
<span class="n">name</span> <span class="o">=</span> <span class="n">names</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="n">GroupTemplate</span><span class="p">):</span>
<span class="nb">object</span><span class="o">.</span><span class="n">writeXML</span><span class="p">(</span><span class="nb">file</span><span class="p">,</span> <span class="n">memo</span><span class="p">)</span>
<span class="n">subgroups</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">name</span><span class="p">,</span> <span class="nb">object</span><span class="p">))</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">atoms</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">name</span><span class="p">,</span> <span class="nb">object</span><span class="p">))</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'<molecule id="</span><span class="si">%s</span><span class="s">"></span><span class="se">\n</span><span class="s">'</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">)</span>
<span class="k">for</span> <span class="n">name</span><span class="p">,</span> <span class="n">subgroup</span> <span class="ow">in</span> <span class="n">subgroups</span><span class="p">:</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">' <molecule ref="</span><span class="si">%s</span><span class="s">" title="</span><span class="si">%s</span><span class="s">"/></span><span class="se">\n</span><span class="s">'</span>
<span class="o">%</span> <span class="p">(</span><span class="n">subgroup</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">name</span><span class="p">))</span>
<span class="k">if</span> <span class="n">atoms</span><span class="p">:</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">' <atomArray></span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="k">for</span> <span class="n">name</span><span class="p">,</span> <span class="n">atom</span> <span class="ow">in</span> <span class="n">atoms</span><span class="p">:</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">' <atom title="</span><span class="si">%s</span><span class="s">" elementType="</span><span class="si">%s</span><span class="s">"/></span><span class="se">\n</span><span class="s">'</span>
<span class="o">%</span> <span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">atom</span><span class="o">.</span><span class="n">element</span><span class="p">))</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">' </atomArray></span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">bonds</span><span class="p">:</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">' <bondArray></span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="k">for</span> <span class="n">a1</span><span class="p">,</span> <span class="n">a2</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">bonds</span><span class="p">:</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">' <bond atomRefs2="</span><span class="si">%s</span><span class="s"> </span><span class="si">%s</span><span class="s">"/></span><span class="se">\n</span><span class="s">'</span>
<span class="o">%</span> <span class="p">(</span><span class="s">':'</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">a1</span><span class="p">),</span> <span class="s">':'</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">a2</span><span class="p">)))</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">' </bondArray></span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'</molecule></span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="n">memo</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="bp">True</span>
<span class="k">def</span> <span class="nf">getXMLAtomOrder</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="n">atom_names</span> <span class="o">=</span> <span class="p">[]</span>
<span class="n">names</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="p">)</span><span class="o">*</span><span class="p">[</span><span class="bp">None</span><span class="p">]</span>
<span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">names</span><span class="p">:</span>
<span class="n">names</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">names</span><span class="p">[</span><span class="n">name</span><span class="p">]]</span> <span class="o">=</span> <span class="n">name</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="p">)):</span>
<span class="n">oname</span> <span class="o">=</span> <span class="n">names</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
<span class="nb">object</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="n">GroupTemplate</span><span class="p">):</span>
<span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="nb">object</span><span class="o">.</span><span class="n">getXMLAtomOrder</span><span class="p">():</span>
<span class="n">atom_names</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">oname</span> <span class="o">+</span> <span class="s">':'</span> <span class="o">+</span> <span class="n">name</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">atom_names</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">oname</span><span class="p">)</span>
<span class="k">return</span> <span class="n">atom_names</span>
<span class="c">#</span>
<span class="c"># The MoleculeFactory class</span>
<span class="c">#</span>
<div class="viewcode-block" id="MoleculeFactory"><a class="viewcode-back" href="../../modules.html#MMTK.MoleculeFactory.MoleculeFactory">[docs]</a><span class="k">class</span> <span class="nc">MoleculeFactory</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> MoleculeFactory</span>
<span class="sd"> A MoleculeFactory serves to create molecules without reference to database</span>
<span class="sd"> definitions. Molecules and groups are defined in terms of atoms, groups, and</span>
<span class="sd"> bonds. Each MoleculeFactory constitutes an independent set of definitions.</span>
<span class="sd"> Definitions within a MoleculeFactory can refer to each other.</span>
<span class="sd"> Each MoleculeFactory stores a set of :class:`~MMTK.ChemicalObjects.Group`</span>
<span class="sd"> objects which are referred to by names. The typical operation sequence is to</span>
<span class="sd"> create a new group and then add atoms, bonds, and subgroups. It is also</span>
<span class="sd"> possible to define coordinates and arbitrary attributes (in particular for</span>
<span class="sd"> force fields). In the end, a finished object can be retrieved as a </span>
<span class="sd"> :class:`~MMTK.ChemicalObjects.Molecule` object.</span>
<span class="sd"> '''</span>
<span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">groups</span> <span class="o">=</span> <span class="p">{}</span>
<span class="bp">self</span><span class="o">.</span><span class="n">locked_groups</span> <span class="o">=</span> <span class="p">{}</span>
<div class="viewcode-block" id="MoleculeFactory.createGroup"><a class="viewcode-back" href="../../modules.html#MMTK.MoleculeFactory.MoleculeFactory.createGroup">[docs]</a> <span class="k">def</span> <span class="nf">createGroup</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Create a new (initially empty) group object.</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="o">.</span><span class="n">has_key</span><span class="p">(</span><span class="n">name</span><span class="p">):</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"redefinition of group "</span> <span class="o">+</span> <span class="n">name</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="n">GroupTemplate</span><span class="p">(</span><span class="n">name</span><span class="p">)</span>
</div>
<div class="viewcode-block" id="MoleculeFactory.addSubgroup"><a class="viewcode-back" href="../../modules.html#MMTK.MoleculeFactory.MoleculeFactory.addSubgroup">[docs]</a> <span class="k">def</span> <span class="nf">addSubgroup</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">group</span><span class="p">,</span> <span class="n">subgroup_name</span><span class="p">,</span> <span class="n">subgroup</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Add a subgroup to a group</span>
<span class="sd"> :param group: the name of the group</span>
<span class="sd"> :type group: str</span>
<span class="sd"> :param subgroup_name: the name of the subgroup within the group</span>
<span class="sd"> :type subgroup_name: str</span>
<span class="sd"> :param subgroup: the subgroup type</span>
<span class="sd"> :type subgroup: str</span>
<span class="sd"> """</span>
<span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">[</span><span class="n">group</span><span class="p">]</span><span class="o">.</span><span class="n">addSubgroup</span><span class="p">(</span><span class="n">subgroup_name</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">[</span><span class="n">subgroup</span><span class="p">])</span>
</div>
<div class="viewcode-block" id="MoleculeFactory.addAtom"><a class="viewcode-back" href="../../modules.html#MMTK.MoleculeFactory.MoleculeFactory.addAtom">[docs]</a> <span class="k">def</span> <span class="nf">addAtom</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">group</span><span class="p">,</span> <span class="n">atom_name</span><span class="p">,</span> <span class="n">element</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Add an atom to a group</span>
<span class="sd"> :param group: the name of the group</span>
<span class="sd"> :type group: str</span>
<span class="sd"> :param atom_name: the name of the atom</span>
<span class="sd"> :type atom_name: str</span>
<span class="sd"> :param element: the chemical element symbol</span>
<span class="sd"> :type element: str</span>
<span class="sd"> """</span>
<span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">[</span><span class="n">group</span><span class="p">]</span><span class="o">.</span><span class="n">addAtom</span><span class="p">(</span><span class="n">atom_name</span><span class="p">,</span> <span class="n">element</span><span class="p">)</span>
</div>
<div class="viewcode-block" id="MoleculeFactory.addBond"><a class="viewcode-back" href="../../modules.html#MMTK.MoleculeFactory.MoleculeFactory.addBond">[docs]</a> <span class="k">def</span> <span class="nf">addBond</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">group</span><span class="p">,</span> <span class="n">atom1</span><span class="p">,</span> <span class="n">atom2</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Add a bond to a group</span>
<span class="sd"> :param group: the name of the group</span>
<span class="sd"> :type group: str</span>
<span class="sd"> :param atom1: the name of the first atom</span>
<span class="sd"> :type atom1: str</span>
<span class="sd"> :param atom2: the name of the second atom</span>
<span class="sd"> :type atom2: str</span>
<span class="sd"> """</span>
<span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">[</span><span class="n">group</span><span class="p">]</span><span class="o">.</span><span class="n">addBond</span><span class="p">(</span><span class="n">atom1</span><span class="p">,</span> <span class="n">atom2</span><span class="p">)</span>
</div>
<span class="k">def</span> <span class="nf">setAttribute</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">group</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">value</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">[</span><span class="n">group</span><span class="p">]</span><span class="o">.</span><span class="n">setAttribute</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">value</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">setPosition</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">group</span><span class="p">,</span> <span class="n">atom</span><span class="p">,</span> <span class="n">vector</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">[</span><span class="n">group</span><span class="p">]</span><span class="o">.</span><span class="n">setPosition</span><span class="p">(</span><span class="n">atom</span><span class="p">,</span> <span class="n">vector</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">getAtomReference</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">group</span><span class="p">,</span> <span class="n">atom</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">[</span><span class="n">group</span><span class="p">]</span><span class="o">.</span><span class="n">getAtomReference</span><span class="p">(</span><span class="n">atom</span><span class="p">)</span>
<div class="viewcode-block" id="MoleculeFactory.retrieveMolecule"><a class="viewcode-back" href="../../modules.html#MMTK.MoleculeFactory.MoleculeFactory.retrieveMolecule">[docs]</a> <span class="k">def</span> <span class="nf">retrieveMolecule</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">group</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param group: the name of the group to be used as a template</span>
<span class="sd"> :type group: str</span>
<span class="sd"> :returns: a molecule defined by the contents of the group</span>
<span class="sd"> :rtype: :class:`~MMTK.ChemicalObjects.Molecule`</span>
<span class="sd"> """</span>
<span class="n">group</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">[</span><span class="n">group</span><span class="p">]</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">makeChemicalObjects</span><span class="p">(</span><span class="n">group</span><span class="p">,</span> <span class="bp">True</span><span class="p">)</span>
</div>
<span class="k">def</span> <span class="nf">makeChemicalObjects</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">template</span><span class="p">,</span> <span class="n">top_level</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">[</span><span class="n">template</span><span class="o">.</span><span class="n">name</span><span class="p">]</span><span class="o">.</span><span class="n">locked</span> <span class="o">=</span> <span class="bp">True</span>
<span class="k">if</span> <span class="n">top_level</span><span class="p">:</span>
<span class="k">if</span> <span class="n">template</span><span class="o">.</span><span class="n">attributes</span><span class="o">.</span><span class="n">has_key</span><span class="p">(</span><span class="s">'sequence'</span><span class="p">):</span>
<span class="nb">object</span> <span class="o">=</span> <span class="n">ChemicalObjects</span><span class="o">.</span><span class="n">ChainMolecule</span><span class="p">(</span><span class="bp">None</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="nb">object</span> <span class="o">=</span> <span class="n">ChemicalObjects</span><span class="o">.</span><span class="n">Molecule</span><span class="p">(</span><span class="bp">None</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="nb">object</span> <span class="o">=</span> <span class="n">ChemicalObjects</span><span class="o">.</span><span class="n">Group</span><span class="p">(</span><span class="bp">None</span><span class="p">)</span>
<span class="nb">object</span><span class="o">.</span><span class="n">atoms</span> <span class="o">=</span> <span class="p">[]</span>
<span class="nb">object</span><span class="o">.</span><span class="n">bonds</span> <span class="o">=</span> <span class="n">Bonds</span><span class="o">.</span><span class="n">BondList</span><span class="p">([])</span>
<span class="nb">object</span><span class="o">.</span><span class="n">groups</span> <span class="o">=</span> <span class="p">[]</span>
<span class="nb">object</span><span class="o">.</span><span class="n">type</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">[</span><span class="n">template</span><span class="o">.</span><span class="n">name</span><span class="p">]</span>
<span class="nb">object</span><span class="o">.</span><span class="n">parent</span> <span class="o">=</span> <span class="bp">None</span>
<span class="n">child_objects</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">child</span> <span class="ow">in</span> <span class="n">template</span><span class="o">.</span><span class="n">children</span><span class="p">:</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">child</span><span class="p">,</span> <span class="n">GroupTemplate</span><span class="p">):</span>
<span class="n">group</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">makeChemicalObjects</span><span class="p">(</span><span class="n">child</span><span class="p">,</span> <span class="bp">False</span><span class="p">)</span>
<span class="nb">object</span><span class="o">.</span><span class="n">groups</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">group</span><span class="p">)</span>
<span class="nb">object</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">group</span><span class="o">.</span><span class="n">atoms</span><span class="p">)</span>
<span class="nb">object</span><span class="o">.</span><span class="n">bonds</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">group</span><span class="o">.</span><span class="n">bonds</span><span class="p">)</span>
<span class="n">group</span><span class="o">.</span><span class="n">parent</span> <span class="o">=</span> <span class="nb">object</span>
<span class="n">child_objects</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">group</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">atom</span> <span class="o">=</span> <span class="n">ChemicalObjects</span><span class="o">.</span><span class="n">Atom</span><span class="p">(</span><span class="n">child</span><span class="o">.</span><span class="n">element</span><span class="p">)</span>
<span class="nb">object</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">atom</span><span class="p">)</span>
<span class="n">atom</span><span class="o">.</span><span class="n">parent</span> <span class="o">=</span> <span class="nb">object</span>
<span class="n">child_objects</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">atom</span><span class="p">)</span>
<span class="k">for</span> <span class="n">name</span><span class="p">,</span> <span class="n">index</span> <span class="ow">in</span> <span class="n">template</span><span class="o">.</span><span class="n">names</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
<span class="nb">setattr</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">child_objects</span><span class="p">[</span><span class="n">index</span><span class="p">])</span>
<span class="n">child_objects</span><span class="p">[</span><span class="n">index</span><span class="p">]</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">name</span>
<span class="k">for</span> <span class="n">name</span><span class="p">,</span> <span class="n">value</span> <span class="ow">in</span> <span class="n">template</span><span class="o">.</span><span class="n">attributes</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
<span class="n">path</span> <span class="o">=</span> <span class="n">name</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">'.'</span><span class="p">)</span>
<span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">namePath</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="n">path</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">]),</span> <span class="n">path</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span> <span class="n">value</span><span class="p">)</span>
<span class="k">for</span> <span class="n">atom1</span><span class="p">,</span> <span class="n">atom2</span> <span class="ow">in</span> <span class="n">template</span><span class="o">.</span><span class="n">bonds</span><span class="p">:</span>
<span class="n">atom1</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">namePath</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="n">atom1</span><span class="p">)</span>
<span class="n">atom2</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">namePath</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="n">atom2</span><span class="p">)</span>
<span class="nb">object</span><span class="o">.</span><span class="n">bonds</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">Bonds</span><span class="o">.</span><span class="n">Bond</span><span class="p">((</span><span class="n">atom1</span><span class="p">,</span> <span class="n">atom2</span><span class="p">)))</span>
<span class="k">for</span> <span class="n">name</span><span class="p">,</span> <span class="n">vector</span> <span class="ow">in</span> <span class="n">template</span><span class="o">.</span><span class="n">positions</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
<span class="n">path</span> <span class="o">=</span> <span class="n">name</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">'.'</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">namePath</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="n">path</span><span class="p">)</span><span class="o">.</span><span class="n">setPosition</span><span class="p">(</span><span class="n">vector</span><span class="p">)</span>
<span class="k">return</span> <span class="nb">object</span>
<span class="k">def</span> <span class="nf">namePath</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">object</span><span class="p">,</span> <span class="n">path</span><span class="p">):</span>
<span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">path</span><span class="p">:</span>
<span class="nb">object</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="n">item</span><span class="p">)</span>
<span class="k">return</span> <span class="nb">object</span>
<span class="k">def</span> <span class="nf">writeXML</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">file</span><span class="p">):</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'<?xml version="1.0" encoding="ISO-8859-1" '</span> <span class="o">+</span>
<span class="s">'standalone="yes"?></span><span class="se">\n\n</span><span class="s">'</span><span class="p">)</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'<templates></span><span class="se">\n\n</span><span class="s">'</span><span class="p">)</span>
<span class="n">memo</span> <span class="o">=</span> <span class="p">{}</span>
<span class="k">for</span> <span class="n">group</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">[</span><span class="n">group</span><span class="p">]</span><span class="o">.</span><span class="n">writeXML</span><span class="p">(</span><span class="nb">file</span><span class="p">,</span> <span class="n">memo</span><span class="p">)</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'</span><span class="se">\n</span><span class="s"></templates></span><span class="se">\n</span><span class="s">'</span><span class="p">)</span></div>
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